Hi,
I have succesfully compiles amber 12 and the corresponding ambertools
Lion with intel c and fortran compilers.
Last time I checked you could still get them as demos for 30 days. I
recommend them for amber.
My two cents.
Sent from my iPhone
On May 20, 2012, at 14:00, amber-request.ambermd.org wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Problem Installing Amber on Mac OSX Lion (Arthur Roberts)
> 2. Electrostatic potential calculation (Sudarshan Debnath)
> 3. Re: Problem Installing Amber on Mac OSX Lion (case)
> 4. Re: Build B form RNA by NAB? (Hai Nguyen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 19 May 2012 20:45:53 -0400
> From: Arthur Roberts <audie.uga.edu>
> Subject: [AMBER] Problem Installing Amber on Mac OSX Lion
> To: <amber.ambermd.org>
> Message-ID: <4FB83EC1.9080108.uga.edu>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> Hi, all,
>
> I followed the instructions on http://jswails.wikidot.com/mac-os-x to
> the letter.
>
> However, I get the following error:
>
> gfortran -c -O3 -mtune=generic -ffree-form -o mbar.o _mbar.f
> cpp -traditional -P -DBINTRAJ bintraj.f > _bintraj.f
> gfortran -c -O3 -mtune=generic -ffree-form -o bintraj.o _bintraj.f
> _bintraj.f:403.25:
>
> call checkerror(nf90_put_att(vel_ncid, VelocVarID,
> "scale_factor", &
> 1
> Error: Generic function 'nf90_put_att' at (1) is not consistent with a
> specific intrinsic interface
> make[1]: *** [bintraj.o] Error 1
> make: *** [serial] Error 2
>
> I checked the gcc and gfortran versions:
>
> bash-3.2$ gcc --version
> gcc (GCC) 4.4.7
> Copyright (C) 2010 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There
> is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
>
> bash-3.2$ gfortran --version
> GNU Fortran (GCC) 4.4.7
> Copyright (C) 2010 Free Software Foundation, Inc.
>
> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
> You may redistribute copies of GNU Fortran
> under the terms of the GNU General Public License.
> For more information about these matters, see the file named COPYING
>
> The active port version is shown:
> bash-3.2$ port select --list gcc
> Available versions for gcc:
> gcc42
> llvm-gcc42
> mp-gcc44 (active)
> none
>
> I appreciate your help.
>
> Sincerely,
> Audie
>
>
> --
> Dr. Arthur "Audie" Roberts, Ph.D.
> University of Georgia
> Department of Pharmaceutical and Biomedical Sciences
> 250 W. Green St.
> Pharmacy South, Room 424
> Athens, GA 30602
> email: audie.uga.edu
> alt: aroberts99163.yahoo.com
> office: 706-542-7787
> lab: 706-542-5979
> fax: 706-542-5358
> cell: 206-850-7468
> skype=aroberts92122
> For urgent matters, text me at 206-850-7468.
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: 20 May 2012 09:27:58 -0000
> From: "Sudarshan Debnath" <sudarshandebnath.ku.rediffmail.com>
> Subject: [AMBER] Electrostatic potential calculation
> To: <amber.ambermd.org>
> Message-ID: <20120520092758.7160.qmail.f4mail-235-144.rediffmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Amber Community (specially Ray, Qin, Case, Gehrcke),
>
> Manny many thanks everybody. I successfully generate the
> electrostatic potential surface in Amber Tools 1.5 and visualized it
> in PyMol. By the way I need some reference (Journal or Book Chapter
> or others) corresponding to the linear and non-linear Poisson-
> Boltzmann equation solvation, salt effect i.e. Poisson-Boltzmann
> equation related. I want to understand the physical significance
> more deeply. If any one send me the references it will be very
> helpful. It is my prominent request.
>
> Best regards,
> Sudarshan.
>
> ------------------------------
>
> Message: 3
> Date: Sun, 20 May 2012 07:52:49 -0400
> From: case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Problem Installing Amber on Mac OSX Lion
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120520115249.GA45383.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Sat, May 19, 2012, Arthur Roberts wrote:
>>
>> However, I get the following error:
>>
>> gfortran -c -O3 -mtune=generic -ffree-form -o mbar.o _mbar.f
>> cpp -traditional -P -DBINTRAJ bintraj.f > _bintraj.f
>> gfortran -c -O3 -mtune=generic -ffree-form -o bintraj.o _bintraj.f
>> _bintraj.f:403.25:
>>
>> call checkerror(nf90_put_att(vel_ncid, VelocVarID,
>> "scale_factor", &
>> 1
>> Error: Generic function 'nf90_put_att' at (1) is not consistent
>> with a
>> specific intrinsic interface
>
> There have been two separate reports about this on Lion. The full
> line
> in bintraj.F90 is
>
> call checkNCerror(nf90_put_att(vel_ncid, VelocVarID, "scale_factor", &
> 20.455), "define velocity scale_factor")
>
> I don't have Lion myself, but suggest putting quotes around "20.455"
> to see
> if that helps. (Lack of quotes seems to be the distinguishing
> feature of this
> call to nf90_put_att compared to all the others.
>
> (Similar instructions for earlier versions of Amber.)
>
> Of course, this will have to be tested for functionality as well.
>
> ....dac
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 20 May 2012 11:09:56 -0400
> From: Hai Nguyen <nhai.qn.gmail.com>
> Subject: Re: [AMBER] Build B form RNA by NAB?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>
> <CAFNMPM9mEsyxbz3UwnN9k7o_B=LBPjoLdyQWnHx717cPsz1H_Q.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks Vlad,
>
> Hai
>
>
> On Sat, May 19, 2012 at 12:48 PM, Vlad Cojocaru <
> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
>> Hi Hai,
>>
>> Well I dont know if you can build B RNA with NAB but what you can
>> do is
>> build a BDNA, modify the PDB and change all the residue names to RNA
>> specific names (A -> RA, T -> RU, G -> RG,, C -> RC), adapt each T
>> to be
>> a U (remove the methyl group), load the resulting PDB into Leap which
>> will add 2'OH groups to all your nts.
>>
>> Of course, you can do all modifications manually, but probably
>> you'd be
>> better of if you write a shell script (based on sed, grep and other
>> useful commands) to do them for you.
>>
>> Hope this helps
>>
>> Best
>> Vlad
>>
>> On 05/19/2012 06:01 PM, Hai Nguyen wrote:
>>> Dear Amber experts,
>>> My apology if the answer for my question is obvious. However, I
>>> can not
>>> find it by myself.
>>>
>>> Best
>>> Hai Nguyen
>>>
>>> On Tue, May 15, 2012 at 1:36 AM, Hai Nguyen<nhai.qn.gmail.com>
>>> wrote:
>>>
>>>> Dear Amber experts,
>>>>
>>>> I want to build a series of B form RNA to perform MD simulations
>>>> showing
>>>> the conversion from B to A form. However, I can not find a NAB
>>>> input to
>>>> build B form RNA (although I can easily build A and B forms for
>>>> DNA and
>> A
>>>> form for RNA by a simple NAB input). I've read the Ambertool
>>>> manual but
>>>> can't find an easy way to do so (or I may accidentally skip that
>> section).
>>>> For a single B-RNA structure, I often use this server
>>>> http://structure.usc.edu/make-na/server.html. However, it's really
>>>> laborious to build few tens of structures in that way. I really
>> appreciate
>>>> if you can give me any suggestion. Thanks.
>>>>
>>>> Best
>>>> Hai Nguyen
>>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>> Dr. Vlad Cojocaru
>> Max Planck Institute for Molecular Biomedicine
>> Department of Cell and Developmental Biology
>> R?ntgenstrasse 20, 48149 M?nster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>
>>
>>
>> _______________________________________________
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Received on Sun May 20 2012 - 16:30:03 PDT
